Re: cell size

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Dec 13 2011 - 08:21:18 CST

On Tue, Dec 13, 2011 at 9:10 AM, Hasan haska <hasanhaska_at_yahoo.com> wrote:
> Dear Namd Users,
>
> I run 5 ns md simulation for water molecules with the conf file below. And I
> want to get the final coordinates of all water molecules in defined cell
> sizes ( 40 40 65 ) . How can I do this operation in NAMD ?

don't use a flexible cell?

axel.

>
> Thank you very much for your help.
>
> Regards.
>
> *********
> #--- This is a test namd configuration file
>
> paratypeCharmm  on
> parameters    water.prm
>
> structure              water.psf
> coordinates            water.pdb
> outputName             water_1out
>
> set temperature    300
> temperature $temperature
>
>
> firsttimestep      0
>
> # Integrator Parameters
> timestep            1
> nonbondedFreq       1
> fullElectFrequency  5
> stepspercycle       10
>
>
>
>
> # Force-Field Parameters
> exclude        scaled1-4
> 1-4scaling    0.8333333
> cutoff          19.7
> switching       on
> switchdist      17
> pairlistdist    24
>
>
>
> # Constant Temperature Control
> langevin            on    ;# do langevin dynamics
> langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
> langevinTemp        $temperature
> langevinHydrogen    on    ;# don't couple langevin bath to hydrogens
>
>
> #--- PBC
>
>
> cellBasisVector1  40. 0.0  0.0
> cellBasisVector2  0.0  40.  0.0
> cellBasisVector3  0.0  0.0  65.
>
> #--- PME
>
> dielectric      1
> PME             on
> PMEGridSizeX    45
> PMEGridSizeY    45
> PMEGridSizeZ    72
>
> # Constant Preswaterre Control (variable volume)
> useGroupPressure   no
> useFlexibleCell       yes
> useConstantArea       yes
>
> langevinPiston        on
> langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
> langevinPistonPeriod  200.
> langevinPistonDecay   100.
> langevinPistonTemp    $temperature
>
>
> #--- Output & Restart
>
> binaryoutput    no
>
> binaryrestart   yes
>
> restartname     water_restart
> DCDfile         water_out.dcd
>
>
> restartfreq        1250
> dcdfreq            1250
> xstFreq            1250
> outputEnergies     1250
> forceDCDfreq       1250
> outputPressure     1250
> outputtiming       1250
>
> minimize 12500
> reinitvels          $temperature
>
> run 5000000
>
> *************

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.

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